Sequencing technologies and genome sequencing | Journal of Applied Genetics
... small RNA, and ChIP-Seq. paired-end sequencing and methylation. ... This cycle and the process were repeated to determine the next ... RNA sequencing. HT-NGS is also finding application in the study of small RNAs. For example, a comprehensive study of miRNA in ... 2010), as well as annotation and discovery of small RNAs from transcriptomic data (Yang et al. 2011). RNA seq using Illumina ... non-coding RNAs and small RNAs, (2) to determine the transcriptional structure of genes, in terms of their start sites, 5- and ...
Analysis of the quinoa genome reveals conservation and divergence of the flowering pathways | Functional & Integrative Genomics
2015). The yield of a crop plant is majorly governed by flowering process as it is the first step towards seed formation. ... 2017). For example FLOWERING CONTROL LOCUS A (FCA) and FPA are RNA-recognition proteins which regulate 3′-end formation, ... The original version of this article was revised: Owing to an error in the production process the above article was published ... Improved understanding and subsequent modification of the flowering process, including flowering time, ensuring high yields, is ...
ALMS1 and Alström syndrome: a recessive form of metabolic, neurosensory and cardiac deficits | Journal of Molecular Medicine
a ALMS1 has been implicated in anchoring the centrosome cohesion protein C-Nap1/CEP250 to centriole proximal ends [21], akin to ... Other AP-MS studies have identified ALMS1 as a possible binding partner of the RNA polymerase II (RNAPII) subunit RPB1 [77]; ... Malicki JJ, Johnson CA (2016) The cilium: cellular antenna and central processing unit. Trends Cell Biol 27:126-140 ... 2). RNAi data have implicated ALMS1 in the proximal end-recruitment of CEP250/C-Nap1 [21], a protein that anchors the ...
A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis)...
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO (2013) The SILVA ribosomal RNA gene database ... Raw data of paired-end sequence read of bacterial and archaeal 16S rRNA gene amplicon sequences are available at the Sequence ... Especially the latter often play a critical role in the processing of food uptake but can also affect host metabolism, host ... Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glockner FO (2013) Evaluation of general 16S ribosomal RNA gene ...
Micro fluorescence in situ hybridization (μFISH) for spatially multiplexed analysis of a cell monolayer | Biomedical...
Schematic of key process steps in conventional FISH and in μFISH. a Using a pipette in conventional FISH, CEP7 probes are ... At the end of probe incubation, we stopped the flow of FISH probes in the inner two apertures, whereas the flow of shaping ... Microfluidic Approaches to Fluorescence In Situ Hybridization (FISH) for Detecting RNA Targets in Single Cells Chapter © 2016 ... After post-processing, an endpoint observation is made. b In μFISH implemented with an MFP, CEP7 probes are localized on ...
Splenic Ly6Chi monocytes contribute to adverse late post-ischemic left ventricular remodeling in heme oxygenase-1 deficient...
The end products of its enzymatic activity possess anti-oxidative, anti- ... Nevertheless, at the end of experiment (day 21) the number of SKL cells was higher in Hmox1−/− mice compared to their WT ... Total RNA isolation, reverse transcription and quantitative PCR. Pieces of tissue from infarct area of the hearts and ... All these observations support a hypothesis, that the process of generation and liberation of monocytes from the spleens of ...
Leaf-chewing herbivores affect preference and performance of a specialist root herbivore | Oecologia
From this ground tissue, RNA was extracted using the Isolate II Plant RNA kit (Bioline) and converted to cDNA using the ... To this end, we treated plants as above with six species of leaf herbivores that were prevented from moving to other leaves by ... Boxes were stored at 7 °C until further processing. Eggs were separated from sand by flotation using a Fenwick can and a 500 µm ... e Shoot dry weight at the end of the experiment. Leaf herbivores were placed on plants 2 days prior to D. radicum infestation ...
NPD1 Plus RvD1 Mediated Ischemic Stroke Penumbra Protection Increases Expression of Pro-homeostatic Microglial and Astrocyte...
Total RNA was prepared using RNeasy columns (Cat. #74004, Qiagen, Valencia, CA). RNA quantity and purity were assessed using ... Genes involved in key signaling processes after stroke, including Il-10, Il-12, Hmgb1, Il-13, p38 MAPK, HIF1α, Stat3, and Il-4 ... A next step is to assess the proteins of each because posttranscriptional changes might modify the end products. Also, the ... Sample Collection and RNA Isolation. Brain samples of the anterior and posterior ipsilesional cortex and subcortex regions were ...
A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems | BMC Bioinformatics
3) identifying referential relations between a syntactic argument of a predicate and the actual target expected in the relation ... The whole process will communicate with users in an interactive way, which we expect is able to further speed up the ... This search procedure ends when we exhaust all possibilities. As a result, more than one pair may be created and all pairs are ... to be an RNA. These examples show that argument types in the trigger specification are essential to the framework to achieve a ...
Resveratrol ameliorates high-glucose-induced hyperpermeability mediated by caveolae via VEGF/KDR pathway | SpringerLink
Briefly, total RNA was extracted by TRIZOL according to the manufacturers instructions and quantified by UV spectrophotometry ... Retention or accumulation of modified macromolecules like lipoproteins and advanced glycation end products (AGE) in the ... there are evidences indicating that caveolae was indispensable to the process, and it was suggested that VEGF-induced ... After the treatment with different doses of RSV for 72 h, respectively, the cells were detached and lysed for total RNA and ...
De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein...
Kanai Y, Dohmae N, Hirokawa N. Kinesin transports RNA: isolation and characterization of an RNA-transporting granule. Neuron. ... Toward this end, we created a "disrupted ASD network," using the 507 disrupted interactions identified in ASD probands as PPI ... i CTS-DAWN genes are enriched in neurodevelopmental processes. The top 10 enriched GO terms of each cell type are shown (FDR ≤ ... Werling D, Pochareddy S, Choi J, An JY, Sheppard B, Peng M, Li Z, Dastmalchi C, Santperebaro G, Sousa A. Whole-genome and RNA ...
Reciprocal Interaction of Cancer Stem Cells of Cholangiocarcinoma with Macrophage | Stem Cell Reviews and Reports
RNA Sequencing Data Analysis. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In ... Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome ... RNA was extracted according to the manufactures instruction of RNA extraction kit (Qiagen). Messenger RNA was purified from ... The processed RNA-seq dataset were deposited at the NCBIs Gene expression omnibus (GEO) data repository. The remaining data ...
Grafting for combinatorial binary model using frequent itemset mining | Data Mining and Knowledge Discovery
Toward this end, we focus on the framework of sparse learning (Rish and Grabarnik 2014) by the \(L_1\)-regularizer, which we ... SVC achieved the best accuracy on fourclass (Ho and Kleinberg 1996), ijcnn1 (Prokhorov 2001) and cod-rna (Andrew et al. 2006); ... Adv Neural Inf Process Syst 30:4765-4774. Google Scholar *. Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O ... Among them, our method performed significantly better on ijcnn1, cod-rna and covtype.binary. Our method extracts features based ...
High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances...
Further reductions in processing cost can be achieved by limiting the number of DNA extractions. This can be done by pooling ... B) Throughput can be increased with the use of inline barcodes (light green and indigo) attached to the 5′-end of the first- ... Edgar RC (2018) Updating the 97% identity threshold for 16S ribosomal RNA OTUs. Bioinformatics 34:2371-2375 ... However, processing all specimens individually still amounts to a considerable workload and cost. Metabarcoding offers a simple ...
Evaluating temperature-induced regulation of a ROSE-like RNA-thermometer for heterologous rhamnolipid production in Pseudomonas...
As such, this work constitutes an important step towards the utilization of temperature-based process designs and enables the ... In the recent past, the presence and function of a ROSE-like RNA-thermometer located in the 5′UTR of the rhamnosyltransferase ... of this native RNA-thermometer for heterologous rhamnolipid production was evaluated and its potential application for process ... control experiments unveiled that besides the regulatory effect of the RNA-thermometer, multiple metabolic effects may ...
"Maybe if I stop the drugs, then maybe they'd care?"-hospital care experiences of people who use drugs | Harm Reduction...
laugh) And then I did not end up going and then that left me sicker. You know? But I did not want the nightmare of [name of ... Small W, Milloy M, McNeil R, Maher L, Kerr T. Plasma HIV-1 RNA viral load rebound among people who inject drugs receiving ... For many in this study, the process of accessing, or being denied, pain management had an overriding impact on the experience ... it was just, lack of it [drugs] being there, and I knew that Id probably end up there [in hospital] again. So you do not want ...
100 years poliovirus: from discovery to eradication. A meeting report | SpringerLink
Particles with variable RNA content and no visible RNA outside may indicate hydrolysis of externalized RNA. According to the ... Up to the end of 2002, the city authorities performed routine vaccination with OPV. However, for the 3 years from the start of ... PV is an excellent model for studying the processes involved. However, the high ratio between physical and infectious particles ... T7 RNA polymerase was used to transcribe the DNA into RNA, which was then added to a cell-free extract of HeLa cells. ...
Genetic and environmental factors of schizophrenia and autism spectrum disorder: insights from twin studies | Journal of Neural...
At the end of the nineteenth century, Francis Golton was the first to consider twins as a useful scientific model, questioning ... DNA methylation, chemical modification of histone proteins, non-coding RNA, and other mechanisms are involved in epigenetic ... conditions arising from long-lasting processes such as aging and maturation are difficult to reproduce when using brain ... non-coding RNA, or neural circuits remodeling, which includes synapse formation, synaptic pruning, microglial regulation, ...
Role of Nrf2/HO-1 system in development, oxidative stress response and diseases: an evolutionarily conserved mechanism |...
... which activate expression of the GATA factors end-1 and end-3 in the E cell [43, 44]. In contrast, in the MS precursor ... This process is regulated by SKN-1 by enhancing DCT-1 expression, a C. elegans homolog of mammalian BNIP3 and BNIP3L/NIX, key ... Seydoux G, Fire A (1994) Soma-germline asymmetry in the distributions of embryonic RNAs in Caenorhabditis elegans. Development ... In D. melanogaster CncA, CncB and CncC have distinct N-terminal end, but share very homologous C-terminus harboring the bZIP (a ...
Islet autoimmunity in human type 1 diabetes: initiation and progression from the perspective of the beta cell | Diabetologia
Type 1 diabetes results from the poorly understood process of islet autoimmunity, which ultimately leads to the loss of ... Single-cell RNA-seq suggested that senescent beta cells in NOD mice upregulate a variety of antigen processing and presentation ... an operating grant from the Health Sciences Centre Foundation Winnipeg and an End Diabetes 2022 Award from Diabetes Canada (OG- ... 1b). Interestingly, the RNA editing enzyme adenosine deaminase RNA specific 1 (ADAR1) is upregulated in response to IFN-α but ...
Case-control meta-analysis of blood DNA methylation and autism spectrum disorder | Molecular Autism
To this end, we have provided our full summary statistics and meta-analysis results. The need for greater sample sizes mimics ... Figures S1-S2. Depiction of surrogate variable selection process for SEED (S1) and SSC (S2). Panel A: Heatmap indicating degree ... RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional ... DNA methylation data quality control (QC) and processing. For the SEED samples, genomic DNA was isolated from 980 whole blood ...